Computation of dna structural variability—a new predictor of dna regulatory regions

Bioinformatics

Volumn 12, Issue 5, 1996, Pages 375-381

  Benham, Craig J ^a  

^a MOUNT SINAI SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DOUBLE STRANDED DNA;

CONFERENCE PAPER; CONFORMATIONAL TRANSITION; DNA REPLICATION; DNA SEQUENCE; DNA STRUCTURE; DNA SUPERCOILING; PRIORITY JOURNAL; STATISTICAL ANALYSIS; SYSTEM ANALYSIS; TRANSCRIPTION INITIATION;

DNA; DNA REPLICATION; DNA, SUPERHELICAL; MATHEMATICAL COMPUTING; MONTE CARLO METHOD; NUCLEIC ACID CONFORMATION; REGULATORY SEQUENCES, NUCLEIC ACID; STATISTICS; TRANSCRIPTION, GENETIC;

EID: 0030451101     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/12.5.375     Document Type: Article

References (11)

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3. Benham, C.J. (1992) Energetics of the strand separation transition in superhelical DNA. J. Mol. Biol, 225, 835-847.
4. Benham.C.J. (1993) Sites of predicted stress-induced DNA duplex destabilization occur preferentially at regulatory loci. Proc. Natl Acad. Sci. USA, 90, 2999-3003.
5. Benham, C.J. (1996) Duplex destabilization in superhelical DNA is predicted to occur at specific transcriptional regulatory regions. J. Mol. Biol., 255, 425-434.
6. Breslauer, K.J., Frank, R., Bloecker, H. and Marky.L.A. (1986) Predicting DNA duplex stability from the base sequence. Proc. Natl Acad. Sci. USA, 83, 3746-3750.
7. Kowalski, D. and Eddy, M.J. (1989) The DNA unwinding element: a novel, cis-acting component that facilitates opening of the Escherichia coli replication origin. EMBO J., 8, 4335-4344.
8. Kowalski, D., Natale.D.A. and Eddy, M.J. (1988) Stable DNA unwinding, not 'breathing', accounts for single-strand-specific nuclease hypersensitivity of specific A + T-rich sequences. Proc. Natl Acad. Sci. USA, 85, 9464-9468.
9. Pulleyblank, D.E., Shure, M., Tang, D., Vinograd.J. and Vosberg, H.-P. (1975) Action of nicking-closing enzyme on supercoiled and nonsupercoiled closed circular DNA: Formation of a Boltzmann Distribution of topoisomers. Proc. Natl Acad. Sci. USA, 72, 4280-4284.
10. Sun, H.-Z., Mezei, M., Fye, R. and Benham, C.J. (1995) Monte Carlo analysis of conformational transitions in superhelical DNA. J. Chem. Phys., 103, 8653-8665.
11. White.J.H. and Bauer, W.R. (1986) Calculation of the twist and the writhe for representative models of DNA. J. Mol. Biol., 189, 329-341.